Cryo-EM structures of Escherichia coli cytochrome bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site

Li, Jiao; Han, Long; Vallese, Francesca; Ding, Ziqiao; Choi, Sylvia K.; Hong, Sangjin; Luo, Yanmei; Liu, Bin; Chan, Chun Kit; Tajkhorshid, Emad; Zhu, Jiapeng; Clarke, Oliver; Zhang, Kai; Gennis, Robert

doi:10.1073/pnas.2106750118

Title: Cryo-EM structures of Escherichia coli cytochrome bo₃ reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site

Journal Article · Fri Aug 20 00:00:00 EDT 2021 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.2106750118· OSTI ID:1849945

Li, Jiao ^[1]; Han, Long ^[2]; Vallese, Francesca ^[3];

^[4];

^[4]; Hong, Sangjin ^[4]; Luo, Yanmei ^[5]; Liu, Bin ^[5]; Chan, Chun Kit ^[4];

^[4];

^[5];

^[3]; Zhang, Kai ^[2];

^[4]

Nanjing Univ. of Chinese Medicine (China); Yale Univ., New Haven, CT (United States)
Yale Univ., New Haven, CT (United States)
Columbia Univ., New York, NY (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States)
Nanjing Univ. of Chinese Medicine (China)

Two independent structures of the proton-pumping, respiratory cytochrome bo3 ubiquinol oxidase (cyt bo₃) have been determined by cryogenic electron microscopy (cryo-EM) in styrene–maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o₃, and Cu_B), the redox-active cross-linked histidine–tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71^I. In both structures, residue H98^I occupies two conformations. In conformation 1, H98^I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98^I has flipped to form a hydrogen bond with E14^I at the N-terminal end of TM0. We propose that H98^I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98^I.

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Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH)

Grant/Contract Number:: FG02-87ER13716; P41GM104601

OSTI ID:: 1849945

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Vol. 118, Issue 34; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Cryo-EM structures of Escherichia coli cytochrome bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site

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Title: Cryo-EM structures of Escherichia coli cytochrome bo₃ reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site